A passenger has suffered serious head injuries and a Melbourne train driver has been stood down following a fight over a cancelled train.

The incident at Flinders Street station on Tuesday came as tenders closed for the contract to run Melbourne's train services for the next eight years.

It is believed the passenger was left with a broken nose and a fractured jaw after approaching the driver aggressively to complain about the train company's service.

Connex spokesman John Rees said the incident happened on platform five at Flinders Street when the 3.33pm (AEST) Werribee train was cancelled.

"We pulled the service because someone had vomited in one of the carriages and it needed to be cleaned. It stemmed from that," he said.

In a statement, Connex managing director Alan Chaplin said the company had removed the driver from duty.

"Police were called when the situation escalated. The driver and another man have given statements to police.

"There will be a full investigation by us and the police. Connex will cooperate fully with the police investigation, including handing over CCTV of the incident.

"We will await the results of our investigation before deciding what further action should be taken, but I can assure our customers that incidents like this are extremely rare."

Mobile phone footage of the incident was aired on a Melbourne news program earlier tonight.

French-owned Connex, French rival Keolis, and Hong Kong's MTR are the three confirmed bidders to run Melbourne's privatised train services for eight years, with an option of a further seven years, from December 1.

Tenders closed on Tuesday afternoon.

Bad publicity caused by reliability problems may increase pressure on the Victorian Government to consider dumping Connex and selecting a new operator.